Janeway comes to an agreement with the Collective. She will stay aboard the Borg cube to develop the weapon against Species 8472 while Voyager is escorted safely through Borg territory. After Tuvok beams over to assist her, the Borg try to install temporary neuro-transceivers on both of them, but Janeway insists they be assigned a Borg representative to communicate with verbally instead. The Borg select a human female drone, designated as "Seven of Nine."

The crew discovers that Species 8472 and their bio-ships are made of the same organic material; both will be vulnerable to the nanoprobes. They plan a large-scale delivery system using Voyager's photon torpedoes. Back in Sickbay, the Doctor cures Kim with the modified nanoprobes. Not long after, a bio-ship attacks, and the Borg protect Voyager. With the Borg cube damaged, Janeway and Tuvok are beamed to Voyager, along with Seven of Nine.

Janeway is injured in the attack, so Chakotay takes charge of Voyager. Despite the Captain's plea to maintain their alliance with the Borg, he balks when Seven of Nine tells him he must travel deeper into Borg space to link up with their nearest ship. Unwilling to travel in the wrong direction, Chakotay decides to drop off the Borg and the nanoprobes at the nearest uninhabited planet and continue through the Delta Quadrant on their own.

Seven of Nine and the other drones seize control of Voyager and send it through an interdimensional rift into fluidic space, the domain of Species 8472. The Borg have been there before; they started the war with 8472 but didn't bargain on their resistance to assimilation. Janeway orders Chakotay to cooperate with Seven of Nine to engage the aliens in fluidic space.

Voyager launches the nanoprobe torpedoes, forcing 8472 to retreat. With their victory complete, Seven of Nine says the Voyager crew will be assimilated. But Janeway and Chakotay had anticipated this. He distracts her long enough for Torres to create a power surge that severs Seven of Nine's connection to the Borg. Feeling responsible for her fate, Janeway opts to keep her onboard in the hope that they can restore her humanity.